Self-programmed enzyme phase separation and multiphase coacervate droplet organization

Membraneless organelles are phase-separated droplets that are dynamically assembled and dissolved in response to biochemical reactions in cells. Complex coacervate droplets produced by associative liquid–liquid phase separation offer a promising approach to mimic such dynamic compartmentalization. Here, we present a model for membraneless organelles based on enzyme/polyelectrolyte complex coacervates able to induce their own condensation and dissolution. We show that glucose oxidase forms coacervate droplets with a cationic polysaccharide on a narrow pH range, so that enzyme-driven monotonic pH changes regulate the emergence, growth, decay and dissolution of the droplets depending on the substrate concentration. Significantly, we demonstrate that time-programmed coacervate assembly and dissolution can be achieved in a single-enzyme system. We further exploit this self-driven enzyme phase separation to produce multiphase droplets via dynamic polyion self-sorting in the presence of a secondary coacervate phase. Taken together, our results open perspectives for the realization of programmable synthetic membraneless organelles based on self-regulated enzyme/polyelectrolyte complex coacervation.

Self-programmed enzyme phase separation is exploited to assemble dynamic multiphase coacervate droplets via spontaneous polyion self-sorting under non-equilibrium conditions.     

Coacervate formation studied by explicit solvent coarse-grain molecular dynamics with the Martini model

Complex coacervates are liquid–liquid phase separated systems, typically containing oppositely charged polyelectrolytes. They are widely studied for their functional properties as well as their potential involvement in cellular compartmentalization as biomolecular condensates. Diffusion and partitioning of solutes into a coacervate phase are important to address because their highly dynamic nature is one of their most important functional characteristics in real-world systems, but are difficult to study experimentally or even theoretically without an explicit representation of every molecule in the system. Here, we present an explicit-solvent, molecular dynamics coarse-grain model of complex coacervates, based on the Martini 3.0 force field. We demonstrate the accuracy of the model by reproducing the salt dependent coacervation of poly-lysine and poly-glutamate systems, and show the potential of the model by simulating the partitioning of ions and small nucleotides between the condensate and surrounding solvent phase. Our model paves the way for simulating coacervates and biomolecular condensates in a wide range of conditions, with near-atomic resolution.

Martini 3 force field can capture the experimental trends of complex coacervates and can be extended to gain physical insight on the mechanisms that drive the formation of LLPS.     

Construction of coacervate-in-coacervate multi-compartment protocells for spatial organization of enzymatic reactions

Coacervate microdroplets, formed via liquid–liquid phase separation, have been extensively explored as a compartment model for the construction of artificial cells or organelles. In this study, coacervate-in-coacervate multi-compartment protocells were constructed using four polyelectrolytes, in which carboxymethyl-dextran and diethylaminoethyl-dextran were deposited on the surface of as-prepared polydiallyldimethyl ammonium/deoxyribonucleic acid coacervate microdroplets through layer-by-layer assembly. The resulting multi-compartment protocells were composed from two immiscible coacervate phases with distinct physical and chemical properties. Molecule transport experiments indicated that small molecules could diffuse between two coacervate phases and that macromolecular enzymes could be retained. Furthermore, a competitive cascade enzymatic reaction of glucose oxidase/horseradish peroxidase–catalase was performed in the multi-compartment protocells. The different enzyme organization and productions of H₂O₂ led to a distinct polymerization of dopamine. The spatial organization of different enzymes in immiscible coacervate phases, the distinct reaction fluxes between coacervate phases, and the enzymatic cascade network led to distinguishable signal generation and product outputs. The development of this multi-compartment structure could pave the way toward the spatial organization of multi-enzyme cascades and provide new ideas for the design of organelle-containing artificial cells.

A coacervate-in-coacervate micro-architecture is constructed as a multi-compartment protocell model, in which a multi-enzyme cascade is spatially organized for competitive enzymatic reactions.     

Interfacial energy of polypeptide complex coacervates measured via capillary adhesion

A systematic study of the interfacial energy (γ) of polypeptide complex coacervates in aqueous solution was performed using a surface forces apparatus (SFA). Poly(L-lysine hydrochloride) (PLys) and poly(L-glutamic acid sodium salt) (PGA) were investigated as a model pair of oppositely charged weak polyelectrolytes. These two synthetic polypeptides of natural amino acids have identical backbones and differ only in their charged side groups. All experiments were conducted using equal chain lengths of PLys and PGA in order to isolate and highlight effects of the interactions of the charged groups during complexation. Complex coacervates resulted from mixing very dilute aqueous salt solutions of PLys and PGA. Two phases in equilibrium evolved under the conditions used: a dense polymer-rich coacervate phase and a dilute polymer-deficient aqueous phase. Capillary adhesion, associated with a coacervate meniscus bridge between two mica surfaces, was measured upon the separation of the two surfaces. This adhesion enabled the determination of the γ at the aqueous/coacervate phase interface. Important experimental factors affecting these measurements were varied and are discussed, including the compression force (1.3-35.9 mN/m) and separation speed (2.4-33.2 nm/s). Physical parameters of the system, such as the salt concentration (100-600 mM) and polypeptide chain length (N = 30, 200, and 400) were also studied. The γ of these polypeptide coacervates was separately found to decrease with both increasing salt concentration and decreasing polypeptide chain length. In most of the above cases, γ measurements were found to be very low, <1 mJ/m(2). Biocompatible complex coacervates with low γ have a strong potential for applications in surface coatings, adhesives, and the encapsulation of a wide range of materials.     

Conductivity and structure of a group of lipid coacervates

Some theories concerning the structure and properties of coacervates are discussed. The preparation of a type of lipid coacervate, suitable as a biological model, especially for olfactory transduction, is described. When organic substances are added, the conductivity of the coacervate decreases roughly in proportion to the amount of additive. The sensitivity to 20 different additives has been investigated. In general, the sensitivity was greater, the longer the chain of the additive. The sensitivity pattern was also dependent on the composition of the coacervate and although the dependence appeared to be very complex, some clear traits could be distinguished. Experimental studies on the optical and diffusional properties and composition of the coacervate are presented. The coacervate was found to be optically isotropic. Its total Na⁺ concentration was about the same as in the equilibrium liquid, whereas the Cl⁻ concentration in coacervate water was lower than in equilibrium liquid. Both remained fairly constant as the coacervate shrank under the influence of added toluene. The diffusion velocities of tartrazine and Sudan black B in coacervate were of the same order of magnitude, which suggests that the lipids may form a continuous network throughout the coacervate phase, rather than discrete micelles.     

Cofilin-Membrane Interactions: Electrostatic Effects in Phosphoinositide Lipid Binding

The actin cytoskeleton interacts with the cell membrane primarily through the indirect interactions of actin-binding proteins such as cofilin-1. The molecular mechanisms underlying the specific interactions of cofilin-1 with membrane lipids are still unclear. Here, we performed coarse-grain molecular dynamics simulations of cofilin-1 with complex lipid bilayers to analyze the specificity of protein-lipid interactions. We observed the maximal interactions with phosphoinositide (PIP) lipids, especially PIP₂ and PIP₃ lipids. A good match was observed between the residues predicted to interact and previous experimental studies. The clustering of PIP lipids around the membrane bound protein leads to an overall lipid demixing and gives rise to persistent membrane curvature. Further, through a series of control simulations, we observe that both electrostatics and geometry are critical for specificity of lipid binding. Our current study is a step towards understanding the physico-chemical basis of cofilin-PIP lipid interactions.     

Structure and characteristics of the complexes between polyampholites and anionic liposomes

Polyampholites are synthesized by the alkylation of poly-4-vinylpyridine with ω-bromocarboxylic acids, and their interaction with the negatively charged bilayer lipid vesicles (liposomes) is studied. In the above polymers, quaternized pyridine units are zwitterion (betaine) groups, in which cationic and anionic groups are linked by the -(CH₂) _n -bridges. Via the methods of fluorescence, laser scattering, and DSC, the length of the ethylene spacer in the betaine group is shown to control the ability of the polymer to interact with anionic liposomes and induce structural rearrangements in the liposomal membrane. At n = 1, polybetaine is not linked to anionic liposomes. At n = 2, polybetaine is sorbed on the membrane, but it causes no dramatic structural rearrangements in the bilayer. At n = 3, the adsorption of polybetaine triggers the lateral segregation of lipids in the outer membrane layer. At n = 5, adsorption of polymer is accompanied by the lateral segregation and flip-flop of lipid molecules; as a result, all anionic membrane lipids are involved in the microphase separation. This evidence is of evident interest for the controlled design of polymers and related complexes and conjugates for biomedical applications.     

Biomolecular and amphiphilic films probed by surface sensitive X-ray and neutron scattering

In this review article we discuss the thin film analytical techniques of interface sensitive X-ray and neutron scattering applied to aligned stacks of amphiphilic bilayers, in particular phospholipid membranes in the fluid L phase. We briefly discuss how the structure, composition, fluctuations and interactions in lipid or synthetic membranes can be studied by modern surface sensitive scattering techniques, using X-rays or neutrons as a probe. These techniques offer an in-situ approach to study lipid bilayer systems in different environments over length scales extending from micrometer to nanometer, both with and without additional membrane-active molecules such as amphiphilic peptides or membrane proteins.     

Counterion-mediated pattern formation in membranes containing anionic lipids

Most lipid components of cell membranes are either neutral, like cholesterol, or zwitterionic, like phosphatidylcholine and sphingomyelin. Very few lipids, such as sphingosine, are cationic at physiological pH. These generally interact only transiently with the lipid bilayer, and their synthetic analogs are often designed to destabilize the membrane for drug or DNA delivery. However, anionic lipids are common in both eukaryotic and prokaryotic cell membranes. The net charge per anionic phospholipid ranges from − 1 for the most abundant anionic lipids such as phosphatidylserine, to near − 7 for phosphatidylinositol 3,4,5 trisphosphate, although the effective charge depends on many environmental factors. Anionic phospholipids and other negatively charged lipids such as lipopolysaccharides are not randomly distributed in the lipid bilayer, but are highly restricted to specific leaflets of the bilayer and to regions near transmembrane proteins or other organized structures within the plane of the membrane. This review highlights some recent evidence that counterions, in the form of monovalent or divalent metal ions, polyamines, or cationic protein domains, have a large influence on the lateral distribution of anionic lipids within the membrane, and that lateral demixing of anionic lipids has effects on membrane curvature and protein function that are important for biological control.     

Electrochemically driven C–N bond formation from CO2 and ammonia at the triple-phase boundary

Electrosynthetic techniques are gaining prominence across the fields of chemistry, engineering and energy science. However, most works within the direction of synthetic heterogeneous electrocatalysis focus on water electrolysis and CO₂ reduction. In this work, we moved to expand the scope of small molecule electrosynthesis by developing a synthetic scheme which couples CO₂ and NH₃ at a gas–liquid–solid boundary to produce species with C–N bonds. Specifically, by bringing in CO₂ from the gas phase and NH₃ from the liquid phase together over solid copper catalysts, we have succeeded in forming formamide and acetamide products for the first time from these reactants. In a subsequent complementary step, we have combined electrochemical analysis and a newly developed operando spectroelectrochemical method, capable of probing the aforementioned gas–liquid–solid boundary, to extract an initial level of mechanistic analysis regarding the reaction pathways of these reactions and the current system''s limitations. We believe that the development and understanding of this set of reaction pathways will play significant role in expanding the community''s understanding of on-surface electrosynthetic reactions as well as push this set of inherently sustainable technologies towards widespread applicability.

Electrocatalytic formation of C–N bonds was achieved through the electrolysis of CO₂ and NH₃ over Cu catalysts. A combined analytical and spectroscopic approach gave insights into the reaction mechanism leading to formamide and acetamide products.     

Photoswitchable Phase Separation and Oligonucleotide Trafficking in DNA Coacervate Microdroplets

Coacervate microdroplets produced by liquid–liquid phase separation have been used as synthetic protocells that mimic the dynamical organization of membrane‐free organelles in living systems. Achieving spatiotemporal control over droplet condensation and disassembly remains challenging. Herein, we describe the formation and photoswitchable behavior of light‐responsive coacervate droplets prepared from mixtures of double‐stranded DNA and an azobenzene cation. The droplets disassemble and reassemble under UV and blue light, respectively, due to azobenzene trans/cis photoisomerisation. Sequestration and release of captured oligonucleotides follow the dynamics of phase separation such that light‐activated transfer, mixing, hybridization, and trafficking of the oligonucleotides can be controlled in binary populations of the droplets. Our results open perspectives for the spatiotemporal control of DNA coacervates and provide a step towards the dynamic regulation of synthetic protocells.     

Molecular determinants of protein-based coacervates

Protein–polyelectrolyte coacervates have gained interest for their potential to stabilize proteins or function as adhesives and their biological implications in the formation of membraneless organelles. To effectively design these materials or predict their biological formation, knowledge of the macromolecular properties that dictate phase separation is required. This review highlights recent advances in the understanding of molecular determinants of protein–polyelectrolyte phase behavior. Properties that promote the phase separation of protein–polyelectrolyte pairs are covered from the perspective of synthetic systems and simplified biological condensates. Prominent factors that determine coacervate formation and material properties include nonspecific intermolecular interactions, as well as specific biological interactions and structures. Here, we summarize the essential roles of electrostatics, including charge magnitude and distribution, (bio)polymer chemistry and structure, and post-translational modifications to protein phase separation in both a synthetic and cellular context.     

Preparation of zinc sodium polyphosphates glasses from coacervates precursors. Characterisation of the obtained glasses, and their applications

A soft chemistry route is described to obtain glasses in the P₂O₅–Na₂O–ZnO–H₂O. It is based on the addition of zinc salts to coacervates prepared from sodium polyphosphate. The processing of these coacervates leads to polyphosphate glasses with the same properties as those of glasses prepared in the classical way. So far, little work has been implemented in this system using ‘coacervate route’. However, it makes an attractive method for coating and joining processes on the industrial scale. As the anion associated to zinc may take part in the adhesion mechanism, coacervate formation has been studied using zinc chloride, nitrate and sulphate as starting materials. The physical properties of the glasses obtained by this method are reported and potential applications of zinc and silver coacervate are described.     

Phase Transitions and Electrochemical Properties of Ionic Liquids and Ionic Liquid—Solvent Mixtures

Recent advances in studies of ionic liquids (IL) and ionic liquid–solvent mixtures are reviewed. Selected experimental, simulation, and theoretical results for electrochemical, thermodynamical, and structural properties of IL and IL-solvent mixtures are described. Special attention is paid to phenomena that are not predicted by the classical theories of the electrical double layer or disagree strongly with these theories. We focus on structural properties, especially on distribution of ions near electrodes, on electrical double layer capacitance, on effects of confinement, including decay length of a dissjoining pressure between confinig plates, and on demixing phase transition. In particular, effects of the demixing phase transition on electrochemical properties of ionic liquid–solvent mixtures for different degrees of confinement are presented.     

G-Protein-Coupled Receptor–Membrane Interactions Depend on the Receptor Activation State

G-protein-coupled receptors (GPCRs) are the largest family of human membrane proteins and serve as primary targets of approximately one-third of currently marketed drugs. In particular, adenosine A₁ receptor (A₁AR) is an important therapeutic target for treating cardiac ischemia–reperfusion injuries, neuropathic pain, and renal diseases. As a prototypical GPCR, the A₁AR is located within a phospholipid membrane bilayer and transmits cellular signals by changing between different conformational states. It is important to elucidate the lipid–protein interactions in order to understand the functional mechanism of GPCRs. Here, all-atom simulations using a robust Gaussian accelerated molecular dynamics (GaMD) method were performed on both the inactive (antagonist bound) and active (agonist and G-protein bound) A₁AR, which was embedded in a 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC) lipid bilayer. In the GaMD simulations, the membrane lipids played a key role in stabilizing different conformational states of the A₁AR. Our simulations further identified important regions of the receptor that interacted distinctly with the lipids in highly correlated manner. Activation of the A₁AR led to differential dynamics in the upper and lower leaflets of the lipid bilayer. In summary, GaMD enhanced simulations have revealed strongly coupled dynamics of the GPCR and lipids that depend on the receptor activation state. © 2019 Wiley Periodicals, Inc.     

Interactions of surfactants and fatty acids with lipids

The recent studies on the interaction of surfactants and fatty acids with lipids are inspired by the want of knowledge from several research fields of highest activity: identification of membrane rafts; membrane protein crystallization; formation of non-lamellar phases in membranes; membrane fusion. Detailed phase diagrams for lipid–surfactant and lipid–fatty acid mixtures, obtained in the last few years, reveal complicated mesomorphic and polymorphic behavior, including miscibility gaps and compound formation. Surfactant-induced non-lamellar to lamellar transitions in lipids and specific temperature-driven bilayer–micelle transitions represent extensions of the general three-stage model of membrane solubilization. Further research is required to construct phase diagrams as to delineate the principles of lipid–surfactant and lipid–fatty acid interactions for the variety of membrane lipid classes.     

Reversible pH-Responsive Coacervate Formation in Lipid Vesicles Activates Dormant Enzymatic Reactions

In situ, reversible coacervate formation within lipid vesicles represents a key step in the development of responsive synthetic cellular models. Herein, we exploit the pH responsiveness of a polycation above and below its pK_a, to drive liquid–liquid phase separation, to form single coacervate droplets within lipid vesicles. The process is completely reversible as coacervate droplets can be disassembled by increasing the pH above the pK_a. We further show that pH-triggered coacervation in the presence of low concentrations of enzymes activates dormant enzyme reactions by increasing the local concentration within the coacervate droplets and changing the local environment around the enzyme. In conclusion, this work establishes a tunable, pH responsive, enzymatically active multi-compartment synthetic cell. The system is readily transferred into microfluidics, making it a robust model for addressing general questions in biology, such as the role of phase separation and its effect on enzymatic reactions using a bottom-up synthetic biology approach.     

Tug-of-war: molecular dynamometers against living cells for analyzing sub-piconewton interaction of a specific protein with the cell membrane

Protein–membrane interactions play important roles in signal transductions and functional regulation of membrane proteins. Here, we design a molecular dynamometer (MDM) for analyzing protein–membrane interaction on living cells. The MDM is constructed by assembling an artificial lipid bilayer and alkylated Cy3-DNA azide (azide-Cy3-Cx) on a silica bubble. After a functional aptamer is covalently anchored onto the corresponding target protein on a living cell through UV irradiation, azide-Cy3-Cx is conjugated with the aptamer through a click reaction to produce a “tug-of-war” between the MDM and the cell due to the buoyancy of the silica bubble. This induces the detachment of the protein from the cell membrane or the alkane terminal from the MDM enabling sub-piconewton embedding force measurement by changing the alkane chain length and simple fluorescence analysis. The successful analysis of embedding force variation of a protein on the cell membrane upon post-translational modifications demonstrates the practicability and expansibility of this method for mechanics-related research in biological systems.

A molecular dynamometer is designed to analyze the variation of sub-piconewton interaction between a specific protein and the membrane on living cells.     

Structural effects of a basic peptide on the organization of dipalmitoylphosphatidylcholine/dipalmitoylphosphatidylserine membranes: a fluorescent resonance energy transfer study

We studied the effect of a model basic peptide, hexalysiltryptophan, on the organization of dipalmitoylphosphatidylcholine/dipalmitoylphosphatidylserine unilamellar vesicles by means of fluorescent resonance energy transfer (FRET) between fluorescently labeled phospholipids. Several FRET theoretical models assuming different bilayer geometries and probe distributions were fitted to the time-resolved data. The experiments were carried out at two temperatures in different regions of the lipid mixture phase diagram. At 45 degrees C, the expected gel/fluid phase separation was verified by model fitting in peptide-free vesicles, which from the FRET approach means that domains are larger than approximately 200 A. No noticeable alteration of membrane organization was detected upon increasing the peptide concentration. At variance, for the single fluid phase at 60 degrees C, there was a large increase in FRET efficiency upon peptide addition to the lipid vesicles, mainly caused by peptide-induced vesicle aggregation. The system gradually changed from unilamellar lipid vesicles to a multibilayer geometry, and a limit lamellar repeat distance of approximately 57 A was recovered. Furthermore, no evidence for lateral domain formation on the FRET length scale was found at this temperature, the cationic peptide being only able to induce local lipid demixing, causing a short-range sequestration of 2-3 acidic lipids around each surface-adsorbed peptide.